A police report has implicated the brother of a former Sri Lankan president saying he directed a top-secret death squad that targeted journalists and dissidents.

The Criminal Investigations Department (CID) told the Mount Lavinia magistrate's court on Monday that Gotabhaya Rajapaksa - who was defence minister during the rule of his brother, Mahinda - led a unit that is accused of assassinating former Sunday Leader newspaper editor Lasantha Wickrematunge.

"Testimony from the former army commander [Sarath Fonseka] shows that there was a special secret unit outside his authority and controlled by Gotabhaya Rajapaksa through the then-chief of national intelligence Kapila Hendawitharana," said the CID report, which was read out in court.

"This unit was operated outside the army command structure and was used to target journalists and other dissidents."

Fonseka - who led Sri Lanka's successful military campaign against Tamil rebels in 2009 - fell out of grace after he unsuccessfully challenged Mahinda Rajapaksa in January 2010 elections.

Wickrematunge's killing, which sparked an international outcry, drew attention to violence against Sri Lanka's media during Rajapaksa's tenure that ended in 2015 when he lost elections to an opposition alliance.

In a written report to the court, CID said a new autopsy revealed that Wickrematunge had been stabbed to death and not shot as previously recorded in the original death certificate.

Wickrematunge's body was exhumed in September for a new forensic test after allegations that the original autopsy report had been falsified to deliberately mislead investigators.

The Mount Lavinia Court ordered police to carry out further investigations and arrest any suspects involved.

Speaking to AFP news agency after Monday's court hearing, a senior police officer said authorities were close to making more arrests over Wickrematunge's murder, after five military intelligence officers were detained last month.

"Now that the cause of death has been firmly established, we can proceed with making further arrests," the officer said on condition of anonymity.

Rajapaksa family

Wickrematunge had accused Gotabhaya of taking kickbacks in arms purchases, including a deal to buy used MiG jet fighters, and was set to testify against him in court when he was killed.

Rajapaksa and several members of his family are under investigation for large-scale fraud and murder during his 10 years as president, in which 17 journalists and media workers were killed.

All deny any wrongdoing and in turn accuse the new government of a political vendetta.

A retired army intelligence officer was found hanging at his home in October with a note claiming responsibility for Wickrematunge's death.

But police have said they do not believe the claim and are treating the officer's death as a murder.